Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line

Abstract

The advanced intercross line (AIL) that is created by successive generations of pseudorandom mating after the F 2 generation is a valuable resource, especially in agricultural livestock and poultry species, because it improves the precision of quantitative trait loci (QTL) mapping compared with traditional association populations by introducing more recombination events. The growth traits of broilers have significant economic value in the chicken industry, and many QTLs affecting growth traits have been identified, especially on chromosomes 1, 4, and 27, albeit with large confidence intervals that potentially contain dozens of genes. To promote a better understanding of the underlying genetic architecture of growth trait differences, specifically body weight and bone development, in this study, we report a nine-generation AIL derived from two divergent outbred lines: High Quality chicken Line A (HQLA) and Huiyang Bearded (HB) chicken. We evaluate the genetic architecture of the F 0 , F 2 , F 8 , and F 9 generations of AIL and demonstrate that the population of the F 9 generation sufficiently randomized the founder genomes and has the characteristics of rapid linkage disequilibrium decay, limited allele frequency decline, and abundant nucleotide diversity. This AIL yielded a much narrower QTL than the F 2 generations, especially the QTL on chromosome 27, which was reduced to 120 Kb. An ancestral haplotype association analysis showed that most of the dominant haplotypes are inherited from HQLA but with fluctuation of the effects between them. We highlight the important role of four candidate genes (PHOSPHO1, IGF2BP1, ZNF652, and GIP) in bone growth. We also retrieved a missing QTL from AIL on chromosome 4 by identifying the founder selection signatures, which are explained by the loss of association power that results from rare alleles. Our study provides a reasonable resource for detecting quantitative trait genes and tracking ancestor history and will facilitate our understanding of the genetic mechanisms underlying chicken bone growth.

The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size

“…Besides, a female phenotype variation of 8.2% for DPW and 6.2% for SL12 was explained by L1. These associations are also consistent with the chicken and duck SNP-based GWAS results, which indicated that SNPs located near IGF2BP1 were associated with body weight, head weight, gizzard weight, chest width, leg weight, and wing weight ( Ma et al 2019 ; Zhou et al 2018 ; Wang, Bu, et al 2020 ; Wang, Cao, et al 2020 ; Zhang, Wang, et al 2021 ). Unexpectedly, L2 allele was not found in the F2 population.…”

“…Since IGF2BP1 was also reported as the body size candidate gene using SNP-based studies ( Sheng et al 2013 ; Ma et al 2019 ; Wang, Bu, et al 2020 ; Wang, Cao, et al 2020 ; Zhang, Wang, et al 2021 ), we explored the SNPs within the region from 10 kb upstream of L1 deletion and 10 kb downstream in order to test whether any of the signal driving SNPs in previous studies could be the causal. SNP calling was done using the same 664 individual sequencing data for building the pan-genome; however, 210 individuals were excluded for the low quality of SNP calling or their heterozygous genotype.…”

“…Many QTGs or QTLs associated with chicken growth traits have been identified, of which loci located at chromosomes 27, 4, and 1 have the largest impact on growth in chicken ( Sheng et al 2013 ; Ma et al 2019 ; Wang, Bu, et al 2020 ; Wang, Cao, et al 2020 ; Zhang, Wang, et al 2021 ). To our knowledge, the study in 2003 was the first time to report that a large QTL region located between 4.0 and 6.1 Mb in chromosome 27 was associated with chicken body size ( Kerje et al 2003 ).…”

“…To our knowledge, the study in 2003 was the first time to report that a large QTL region located between 4.0 and 6.1 Mb in chromosome 27 was associated with chicken body size ( Kerje et al 2003 ). After that, many studies identified the chicken growth trait QTL in chromosome 27, including the gene IGF2BP1 by SNP-based GWAS ( Sheng et al 2013 ; Ma et al 2019 ; Wang, Bu, et al 2020 ; Wang, Cao, et al 2020 ). Our previous GWAS also revealed a signal peak correlated to body size trait, which was located at the genomic upstream of IGF2BP1 ( Zhang, Wang, et al 2021 ).…”

“…Dwarfism and impaired gut development were also observed in IGF2BP1-deficient mice ( Hansen et al 2004 ). Evidence from genome-wide association studies (GWASs) and QTL mapping revealed that the genomic regions upstream of IGF2BP1 were significantly associated with body weight, head weight, gizzard weight, chest width, leg weight, and wing weight in chicken and duck ( Sheng et al 2013 ; Ma et al 2019 ; Zhou et al 2018 ; Wang, Bu, et al 2020 ; Wang, Cao, et al 2020 ; Zhang, Wang, et al 2021 ). However, the causal variations of IGF2BP1 that responsible for body sizes in chicken and duck remain unclear.…”